Family of the Doctor
by GothGirl1996
Summary: Set just after Trenzalore. the 11th Doctor, Clara and the London Gang are dragged forward in the Doctor's timeline where the Great Intelligence makes another appearance and this time he is going to hurt the Doctor through whom he loves most- his family, including the one's he has yet to meet- his family with River. featuring some old friends
1. Chapter 1

Chapter 1

Leaving Trenzalore

Jenny, Strax and Madame Vastra made their way back to the TARDIS following the Doctor and Clara, who lay in his arms, alive but unconscious. When they got in the Doctor carried Clara to her room and lay her down to rest and recover from being in his time stream before he returned to the console room and to Strax, Jenny and Madame Vastra. When he entered and joined them on the control room platform, Jenny ran to him and hugged him. He hugged her back.

"I'm glad you're alive, Doctor." She said kindly flashing him a smile as she released him.

"All thanks to Clara, Jenny. But it is good to be back." He replied and she moved away to hold Vastra's hand. The relationship between them stronger than ever.

"The boy is right, for once, sir. It is nice to have you back." Strax said casting a glance to Jenny and Vastra. Jenny didn't react this time, she couldn't be bothered.

"Thank you, Strax. Home, Vastra?" The Doctor asked then as he danced around the console flicking switches and pushing buttons as he went.

"Please, Doctor." Vastra agreed quietly.

Once they were in the vortex, Clara awoke and made her way to the console room. She found the Doctor sitting on the stairs and Jenny, Vastra and Strax in one corner talking quietly to each other. She sat beside him and leant her head on his shoulder. She looked down at his hands and saw he clutched a blue TARDIS shaped book in his hands, tightly.

"This was River's Diary. We never met in the right order on our time lines. We were going in different directions and only crossing paths once in a while. So we kept diaries to keep a record of our meetings." The Doctor said quietly to Clara.

"Sensible. Did you love her, your wife, River?" Clara asked.

"Yes. I did. Until you discovered my name in the library here in the TARDIS, she was the only one who knew it."

"She opened your tomb?"

"Yes. I just regret not spending more time with her. But because we never met in the right order, we couldn't reveal much to each other. I couldn't know of my future. Our adventures were her past and my future. The first time I met her, was the day she died in the the biggest library in the universe. I didn't know her and I know I broke her heart because of it. I didn't know who she was to me. Her memories then were my future ones..." He explained but spotted Clara's confused face. "It's complicated..." The Doctor was about to continue when the TARDIS roared and lost control as she was dragged off her set course to another part of the universe several pivotal moments into the Doctor's future. All within her were thrown off kilter.

"Doctor!" Clara and Jenny screamed. Jenny grabbing hold of Vastra.

"Sir!" Strax bellowed above the noise and the Doctor grabbed hold of Clara and made his way to the console.

"What's going on, old girl? Hey, where are we going?" Another jerk forward. "Come on Sexy that wasn't nice. SEXY!" The Doctor bellowed as the TARDIS roared once more and was pulled through the Vortex and landed with a shuddering thump on the place where the Doctor would meet his biggest adventure ever.


	2. Chapter 2

Chapter 2

The Great Intelligence returns.

He opened the door to the TARDIS and stepped out, Clara holding his hand tightly. The TARDIS had landed in a large darkened room with a solitary spotlight in the centre where the TARDIS had landed, the spotlight circled it about 5 metres in radius from the TARDIS itself. The Doctor took a small step forward and away from the safety of the TARDIS to allow Vastra, Strax and Jenny ("everyone's favourite Victorian Chambermaid" as the Doctor called her) to join them.

"Where are we?" Jenny asked as the TARDIS doors shut behind her.

"Welcome to my home, Doctor and Friends." Came the disembodied voice of Doctor Simeon.

"Simeon." The Doctor said through clenched teeth, a scowl on his face. "How are you not dust?"

"I am simply the Great Intelligence now, not physical form. Your time stream did that to me but it did not destroy me as you believed it would, Doctor."

"I wasn't sure what was going to happen when you entered my time stream!" The Doctor roared at the disembodied voice of the Great Intelligence.

"Since it would appear that I can't hurt you yourself. I can hurt you through another means. Another means even more precious to you than your own life." The Great Intelligence sneered.

"What means?" Simeon laughed at the Doctor. "WHAT MEANS?" The Doctor roared again at Simeon.

"Your family, Doctor," Simeon said as another spotlight flashed on ahead of them to reveal River Song and a few others gathered together, including his daughter Jenny who he believed had died. "And your friends."

Now the Doctor was stunned as Sarah Jane and her son and his friends, Rose and the Metacrisis Doctor, Donna, Martha and Mickey and Captain Jack Harkness who glared angrily and reached out for a woman who was stood with River.

"Hello, Sweetie." River said nervously, her arms on the shoulders of two boys of about 16 years old. The woman who had been reached for by Jack, pushed a small child, a little girl, behind her beside River.

"Are you okay, River? Where are we?" The Doctor asked referring to their personal timeline.

"We've just lost Amy and Rory. I'm an archeologist in the 51st Century. You?" She asked nervously once more, her gun holstered at her hip.

"Trenzalore. Sorry spoilers. You don't know that part yet." The Doctor explained quickly.

"I'll leave you to say your goodbyes Doctor, before I begin my path of pain." Simeon said as he flooded the room with light- merging the spotlights.


	3. Chapter 3

Chapter 3

Family of the Doctor

Once the room was flooded with light the woman stood with River ran to Jack,, her child in her arms and River made her way to the Doctor, wrapping her arms around his neck in a tight hug.

The Doctor wanted to cry as he hugged her, having only said "goodbye" to her moments ago.

"River, Simeon said something about a family? Do we have a family? Something I never knew?" The Doctor asked her as she pulled away and River nodded.

"Yes, I wanted to tell you but didn't know how. Kate," she addressed the woman with the small child with Jack. The woman turned and made her way over with Jack and her child. "Alistair, John, come here for a moment."

The two boys joined their mother and stood beside her. Both lads were of a similar height, both with dark hair and green eyes. The woman, Kate, was about 20 with dark hair and green eyes too. It was obvious they were siblings.

"Katherine Sarah-Jane, otherwise known as Kate, our eldest. Her husband Jack, you know, and their daughter, Susan. This is Alistair Brian and John Rory our twin sons. Children, your father The Doctor." River explained and Jack stared stunned as Jenny, the Doctor's Daughter ran and embraced her father. Followed by Kate and Susan, Jack and the twins.

"Nice to see you, Doctor. You've changed again." Jack commented as Kate handed Susan to the Doctor who hugged her gently.

"Susan." The Doctor whispered as images of the young woman who was his granddaughter flashed through his mind in memories.

"Ah the family of the Doctor." Simeon said and River, their children, Jsck and the Doctor's friends all gathered around him protectively.

"You won't get him." Kate warned as she took Jack's hand and her brother Alistair's as they were the front line of defence.

"I'm afraid, my dear, I will." Simeon laughed maniacally and Kate stood her ground, River behind her with Jenny, the Doctor's daughter, the Doctor holding Susan and John, Kate's other brother. No one was going to hurt the Family of the Doctor or his friends.


	4. Chapter 4

Chapter 4

Pain

After Simeon spoke Kate was dragged from the group, by some supernatural means and positioned in a single spotlight a little way away from the Doctor and her family. Jack reached for her and she for him to no avail.

"Let her go!" Jack roared and the young Susan in the Doctor's arms whimpered as her mother doubled over in pain and screamed. The Doctor passed Susan over to River who held her tightly and rubbed the child's back soothingly.

"Let my daughter go, Simeon. Stop whatever it is you are doing to her. NOW!" The Doctor roared and Simeon laughed manically. Kate stopped screaming and slumped forward, breathing heavily, her hand in her lower abdomen.

"Kate?" Jack asked as she crawled back to him and he scooped her up to lean into his side.

"He killed him." She whispered as she took Jack's hand to her abdomen indicating that Simeon had killed their child. Jack growled and held onto her tightly. Susan laced her fingers into her mother's cardigan shoulder, holding onto her.

"You want me, Simeon, you got me. You don't have to hurt my children and if you even think of laying a hand on my Wife I will do something really, really bad." The Doctor growled, his hand reaching out for River, who took it tightly in her own and stepping closer to him, having given Susan to Jack.

"How bad could you get Doctor? That is something I would love to see." Simeon said, temptingly.

"River, tell me something... How many time lords are in this room?"

"Seven. Yourself, me, Kate, Alistair, John, Jenny your daughter and Susan. Why?" She asked holding his hand tighter still in her hand.

"How much do you love me?" The Doctor asked now.

"Do I have to prove it?" She teased.

"Yes."

"Very well. Hello, sweetie." She smiled and kissed the Doctor letting the regeneration and life energy of the TARDIS surround them. When they broke apart it disappeared.

"What was that?" Simeon asked concerned and a little scared.

"The love of a timelord, true love's kiss, Simeon. Love. Something I doubt you have even felt. Now imagine that multiplied by all these people here... Powerful stuff." The Doctor winked in Jack's direction. Jack nodded, knowing what he was up to.

"Not everyone in the room is a timelord..."

"No but they all have love for one timelord... me." The Doctor grinned. "And frankly today, I love it, I relish it. Love is good and one of the greatest and most powerful emotions in the universe." He kissed River again, passionately this time. Getting the message, Kate kissed Jack and Susan. Alistair and John both kissed their half sister Jenny's cheeks. And everyone else just thought of every moment they had ever spent with the Doctor and the love they had for him. Rose kissed the Metacrisis Doctor, because he was still her Doctor with his Memories. She loved him just as she loved the Doctor before her at the front of the crowd. Involuntarily Mickey took her hand as she kissed the Metacrisis and he kissed Martha.

Soon the room was filled with love and the energies of the TimeLords. Unbeknownst to Jack and the Doctor, Kate was still bleeding internally from her torture by Simeon, her body was growing weaker and she was dying. After a few moments everyone broke apart and Simeon let out a groan of pain, for their love had allowed the TARDIS to hack into his mainframe and destroy him from the inside out. So. Much so that he was now just a shadow of us former self.

With Simeon practically destroyed the Doctor, Jack and River panicked as Kate fell to her knees and slumped forward looking dangerously unwell.


	5. Chapter 5

Chapter 5

Death of a daughter, a wife and a mother.

Kate felt herself slump forward and Jack bent to her side and lifted her head into his lap. "Kate? Sweetheart?" He asked as he saw blood pooling on her clothes.

"Katherine?" The Doctor asked as he knelt beside her. Martha rushed to their side as River took her daughter's hand and Susan touched her face with a tiny hand.

"She's got internal bleeding, Doctor, there isn't anything I can do, she's too far gone. I'm sorry." Martha said quietly in his ear. He began to cry. He had only just met her, his brave and strong daughter who had blessed him with Susan, his first companion, and now he was loosing her.

"Katherine, stay with me." The Doctor urged, tears in his eyes. River stroked her daughter's hair with her fingers. "Baby stay with me. We could see the stars, and take tea on Mars. Kate?"

"Hello, dad. Nice to see you." Kate choked out painfully. "Don't worry, we'll see each other again.. Mum's past is your future right? We'll meet again. I promise. In the mean time..." She sighed and coughed. "Help Jack and mum care for Susan. I love you, all of you."

"I will but I'm not losing you Kate." The Doctor pleaded.

"Take her to see the stars, Dad. Show her the universe and take me to Galli..." She whispered as she breathed her last. Jack cradled her and cried, Susan cried and River hugged the Doctor as he wept for his newly found daughter was taken from him.

"Take her where?" River asked.

"Gallifrey. But Gallifrey is lost it was destroyed in the time war, River. It is no more." The Doctor said angrily, rising to his feet. Jack picked up Kate's lifeless body and carried her to the TARDIS as River took up Susan in her arms and followed the men accompanied by the Doctor's friends.

"Won't she regenerate?" Clara asked, jogging to keep up with the Doctor.

"No, Clara it was her last regeneration, she won't wake up now." Jack said tearfully, as he laid her on the bench inside the TARDIS. "I like the new interior, Doctor." He added sadly as he stroked her hair off her face.

The TARDIS sounded mournful as she set off into the vortex as she sailed away dropping people home, including the parallel universe for Rose and the Metacrisis. Once everyone apart from Vastra and Jenny the Chambermaid, Strax and Clara, River, Jack, Susan and the twin boys, the Doctor took Susan off River as she took over the reigns on the TARDIS. She flew her to the 51st century.

* * *

The group buried Kate in the grounds of River's home so she would be close to Susan. Was this the new Gallifrey? The Doctor wondered. They toasted over her grave together.

"Katherine Sarah-Jane Harkness-Song, a daughter, a wife and a mother, may she rest in eternal peace." Strax announced as he toasted to her in heaven.

"Kate." The others announced and then all dispersed. River hugging The Doctor tightly.

"I love you and she loved you, you know. I can let you know one spoiler." She whispered in his ear.

"Oh what's that, Professor River Song?" The Doctor teased.

"You will be there for her birth and the birth of the boys and of Susan. You even walked her down the aisle when she married Jack." She whispered once more, her red painted lips quirking into a smile. The Doctor laughed quietly.

"Good to know, Professor. Tell me something else... When you said you were quite a screamer... Did you...?" The Doctor asked indicating what he meant with his eyes and this time River laughed.

"Doctor!" She pretended to scold to him. "Yes, I did." She whispered, kissing him once more.

"I look forward to it. See you around, Professor River Song." He smiled as he backed towards the TARDIS.

"Until the next time, Doctor. Goodbye, Sweetie." She breathed as he disappeared inside the TARDIS and it took off... With the brakes on. River grimaced and smiled as he vanished. She was looking forward to the meeting where Kate was conceived. It had been quite an adventure in itself and now she knew he had the biggest adventure still to come- Parenthood, from the beginning.

Fin


End file.
